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albac-guest pushed a change to branch master
in repository r-cran-phangorn.
from b82b55e Adding explanation of binary files and upload to unstable
new 82e88f6 Imported Upstream version 1.99.14
new df60f7d Update for new upstream version.
The 2 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
DESCRIPTION | 16 +-
MD5 | 79 +--
NAMESPACE | 28 +-
NEWS | 46 ++
R/clanistic.R | 2 +-
R/distSeq.R | 19 +
R/distTree.R | 554 +++++++++++++++++++++
R/fitch.R | 2 +-
R/modelTest.R | 201 ++++++++
R/neighborNet.R | 9 +-
R/networx.R | 20 +-
R/parsimony.R | 10 +-
R/phyDat.R | 58 ++-
R/phylo.R | 1010 +++++++++++----------------------------
R/treeManipulation.R | 1 +
R/treedist.R | 39 +-
README.md | 6 +
TODO | 15 +
build/vignette.rds | Bin 335 -> 335 bytes
debian/changelog | 7 +
debian/control | 8 +-
inst/doc/Networx.R | 14 +-
inst/doc/Networx.Rmd | 2 +-
inst/doc/Networx.html | 2 +-
inst/doc/Trees.R | 2 +-
inst/doc/Trees.Rnw | 2 +-
man/bootstrap.pml.Rd | 5 +-
man/densiTree.Rd | 3 +
man/dist.hamming.Rd | 6 +
man/modelTest.Rd | 7 +-
man/parsimony.Rd | 4 +-
man/phyDat.Rd | 17 +-
man/plot.networx.Rd | 2 +-
man/pml.fit.Rd | 3 +
man/splitsNetwork.Rd | 2 +-
man/treedist.Rd | 3 +-
src/fitch.c | 42 +-
src/ml.c | 495 +++++++++++--------
src/sankoff.c | 2 +-
tests/testthat.R | 4 +
tests/testthat/test_parsimony.R | 21 +
tests/testthat/test_phyDat.R | 19 +
tests/testthat/test_treedist.R | 14 +
vignettes/Networx.Rmd | 2 +-
vignettes/Trees.Rnw | 2 +-
vignettes/phangorn.bib | 203 +++++++-
46 files changed, 1893 insertions(+), 1115 deletions(-)
create mode 100644 R/distTree.R
create mode 100644 R/modelTest.R
create mode 100644 TODO
create mode 100644 tests/testthat.R
create mode 100644 tests/testthat/test_parsimony.R
create mode 100644 tests/testthat/test_phyDat.R
create mode 100644 tests/testthat/test_treedist.R
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